[Go-diff] GO update 08/28/2008

Remote CVS for Gene Ontology gocvs at genome.stanford.edu
Thu Aug 28 21:30:46 PDT 2008 

OBODIFF of gene_ontology_write.obo version 1.184 by 1.185

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0034732
* Created object of type obo:TERM with id GO:0034733
* Created object of type obo:TERM with id GO:0034734
* Created object of type obo:TERM with id GO:0034735
* Created object of type obo:TERM with id GO:0034736
* Created object of type obo:TERM with id GO:0034737
* Created object of type obo:TERM with id GO:0034738
* Created object of type obo:TERM with id GO:0034739
* Created object of type obo:TERM with id GO:0034740
* Created object of type obo:TERM with id GO:0034741
* Created object of type obo:TERM with id GO:0034742
* Created object of type obo:TERM with id GO:0034743
* Created object of type obo:TERM with id GO:0034744
* Created object of type obo:TERM with id GO:0034745
* Populated new object GO:0034732 (macro)
  * Changed name of GO:0034732 from "<new term>" to "transcription factor TFIIIB-alpha complex"
  * Set definition of GO:0034732 to "A transcription factor TFIIIB-beta complex that contains the TATA-binding protein (TBP), B'' and a specialized homolog of the conserved subunit BRF referred to as BRFU or TFIIIB50, which found in human but not conserved in yeast; the complex is involved in the regulation of transcription from type 3 (upstream) RNA polymerase III promoters."
  * Added definition dbxref PMID:11433012 to GO:0034732
  * Copied GO:0034732 to GO:0000126 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034732
* Populated new object GO:0034733 (macro)
  * Changed name of GO:0034733 from "<new term>" to "transcription factor TFIIIB-beta complex"
  * Added comment "Note that the subunits of TFIIIB-beta are conserved between human and yeast; however, in yeast a single TFIIIB complex regulates transcription of tRNA, 5S rRNA and U6 snRNA genes, whereas two different TBP-dependent TFIIIB activities exist in humans."
  * Set definition of GO:0034733 to "A transcription factor TFIIIB-beta complex that contains the TATA-binding protein (TBP), B'' and BRF, and is involved in the regulation of transcription from type 2 RNA polymerase III promoters."
  * Added definition dbxref PMID:11433012 to GO:0034733
  * Copied GO:0034733 to GO:0000126 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034733
* Populated new object GO:0034734 (macro)
  * Changed name of GO:0034734 from "<new term>" to "transcription factor TFIIIC1 complex"
  * Set definition of GO:0034734 to "A transcription factor complex that forms part of the TFIIIC complex, observed in human. The complex is poorly characterized, but contains the 250-kDa form of HsBdp1, and is thought to include nuclear factor 1 (NF1). It stimulates binding by human TFIIIC2 and is required for transcription activity."
  * Added definition dbxref GOC:mah to GO:0034734
  * Added definition dbxref PMID:11433012 to GO:0034734
  * Added definition dbxref PMID:15096501 to GO:0034734
  * Copied GO:0034734 to GO:0000127 with type part_of
  * Copied GO:0034734 to GO:0005667 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034734
* Populated new object GO:0034735 (macro)
  * Changed name of GO:0034735 from "<new term>" to "transcription factor TFIIIC2 complex"
  * Set definition of GO:0034735 to "A transcription factor complex that forms part of the TFIIIC complex, observed in human; composed of five subunits (GTF3C1/hTFIIIC220/TFIIICalpha, GTF3C2/hTFIIIC110/TFIIICbeta, GTF3C3/hTFIIIC102/TFIIICgamma, GTF3C4/hTFIIIC90/TFIIICdelta and GTF3C5/hTFIIIC63/TFIIICepsilon in human) that together recognize the type 2 RNA polymerase III promoter."
  * Added definition dbxref GOC:mah to GO:0034735
  * Added definition dbxref PMID:11433012 to GO:0034735
  * Copied GO:0034735 to GO:0000127 with type part_of
  * Copied GO:0034735 to GO:0005667 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034735
* Populated new object GO:0034736 (macro)
  * Changed name of GO:0034736 from "<new term>" to "cholesterol O-acyltransferase activity"
  * Set definition of GO:0034736 to "Catalysis of the reaction: acyl-CoA + cholesterol = CoA + cholesterol ester."
  * Added definition dbxref EC:2.3.1.26 to GO:0034736
  * Added general dbxref EC:2.3.1.26 to GO:0034736
  * Added general dbxref MetaCyc:STEROL-O-ACYLTRANSFERASE-RXN to GO:0034736
  * Added synonym "ACAT activity" to GO:0034736
  * Added general dbxref EC:2.3.1.26 to synonym ACAT activity of GO:0034736
  * Changed synonym scope of GO:0034736 from "Related" to "Broad"
  * Added synonym "acyl coenzyme A-cholesterol-O-acyltransferase activity" to GO:0034736
  * Added general dbxref EC:2.3.1.26 to synonym acyl coenzyme A-cholesterol-O-acyltransferase activity of GO:0034736
  * Changed synonym scope of GO:0034736 from "Related" to "Exact"
  * Added synonym "acyl-CoA:cholesterol acyltransferase activity" to GO:0034736
  * Added general dbxref EC:2.3.1.26 to synonym acyl-CoA:cholesterol acyltransferase activity of GO:0034736
  * Changed synonym scope of GO:0034736 from "Related" to "Exact"
  * Added synonym "acyl-CoA:cholesterol O-acyltransferase activity" to GO:0034736
  * Added general dbxref EC:2.3.1.26 to synonym acyl-CoA:cholesterol O-acyltransferase activity of GO:0034736
  * Changed synonym scope of GO:0034736 from "Related" to "Exact"
  * Added synonym "acylcoenzyme A:cholesterol O-acyltransferase activity" to GO:0034736
  * Changed synonym scope of GO:0034736 from "Related" to "Exact"
  * Added synonym "cholesterol acyltransferase activity" to GO:0034736
  * Added general dbxref EC:2.3.1.26 to synonym cholesterol acyltransferase activity of GO:0034736
  * Changed synonym scope of GO:0034736 from "Related" to "Broad"
  * Added synonym "cholesterol ester synthetase activity" to GO:0034736
  * Added general dbxref EC:2.3.1.26 to synonym cholesterol ester synthetase activity of GO:0034736
  * Changed synonym scope of GO:0034736 from "Related" to "Exact"
  * Added synonym "cholesterol O-acyltransferase activity" to GO:0034736
  * Changed synonym scope of GO:0034736 from "Related" to "Exact"
  * Added synonym "cholesteryl ester synthetase activity" to GO:0034736
  * Added general dbxref EC:2.3.1.26 to synonym cholesteryl ester synthetase activity of GO:0034736
  * Changed synonym scope of GO:0034736 from "Related" to "Exact"
  * Copied GO:0034736 to GO:0004772 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034736
* Populated new object GO:0034737 (macro)
  * Changed name of GO:0034737 from "<new term>" to "ergosterol O-acyltransferase activity"
  * Set definition of GO:0034737 to "Catalysis of the reaction: acyl-CoA + ergosterol = CoA + ergosterol ester."
  * Added definition dbxref GOC:mah to GO:0034737
  * Added general dbxref EC:2.3.1.26 to GO:0034737
  * Added general dbxref MetaCyc:STEROL-O-ACYLTRANSFERASE-RXN to GO:0034737
  * Copied GO:0034737 to GO:0004772 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034737
* Populated new object GO:0034738 (macro)
  * Changed name of GO:0034738 from "<new term>" to "lanosterol O-acyltransferase activity"
  * Set definition of GO:0034738 to "Catalysis of the reaction: acyl-CoA + lanosterol = CoA + lanosterol ester."
  * Added definition dbxref GOC:mah to GO:0034738
  * Added general dbxref EC:2.3.1.26 to GO:0034738
  * Added general dbxref MetaCyc:STEROL-O-ACYLTRANSFERASE-RXN to GO:0034738
  * Copied GO:0034738 to GO:0004772 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034738
* Populated new object GO:0034739 (macro)
  * Changed name of GO:0034739 from "<new term>" to "histone deacetylase activity (H3-K16 specific)"
  * Set definition of GO:0034739 to "Catalysis of the removal of an acetyl group from lysine at position 16 of the histone H3 protein."
  * Added definition dbxref GOC:mah to GO:0034739
  * Copied GO:0034739 to GO:0004407 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034739
* Populated new object GO:0034740 (macro)
  * Changed name of GO:0034740 from "<new term>" to "TFIIIC-TOP1-SUB1 complex"
  * Set definition of GO:0034740 to "A protein complex that contains TFIIIC, topoisomerase 1, and Sub1/PC4. Characterized in human, the complex is involved in regulating transcription from RNA polymerase III (Pol III) promoters. Topoisomerase 1 and Sub1 enhance the accuracy of transcription termination, and promote reinitiation by Pol III."
  * Added definition dbxref PMID:9660958 to GO:0034740
  * Added synonym "TFIIIC-Topoisomerase 1-PC4 complex" to GO:0034740
  * Changed synonym scope of GO:0034740 from "Related" to "Exact"
  * Copied GO:0034740 to GO:0016591 with type part_of
  * Copied GO:0034740 to GO:0005667 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034740
* Populated new object GO:0034741 (macro)
  * Changed name of GO:0034741 from "<new term>" to "APC-tubulin-IQGAP1 complex"
  * Added comment "Note that the gene/protein name 'APC' should not be confused with the abbreviation for 'anaphase promoting complex'."
  * Set definition of GO:0034741 to "A protein complex that contains the tumor suppressor protein adenomatous polyposis coli (APC), alpha-tubulin, gamma-tubulin, and the Rac1 and Cdc42 effector IQGAP1; may play a role in cytoskeleton organization."
  * Added definition dbxref PMID:17126424 to GO:0034741
  * Added synonym "60S APC complex" to GO:0034741
  * Changed synonym scope of GO:0034741 from "Related" to "Narrow"
  * Copied GO:0034741 to GO:0043234 with type OBO_REL:is_a
  * Copied GO:0034741 to GO:0044444 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034741
* Populated new object GO:0034742 (macro)
  * Changed name of GO:0034742 from "<new term>" to "APC-Axin-1-beta-catenin complex"
  * Added comment "Note that the gene/protein name 'APC' should not be confused with the abbreviation for 'anaphase promoting complex'."
  * Set definition of GO:0034742 to "A protein complex that contains the tumor suppressor protein adenomatous polyposis coli (APC), Axin-1, and beta-catenin."
  * Added definition dbxref PMID:16188939 to GO:0034742
  * Added synonym "23S APC complex" to GO:0034742
  * Changed synonym scope of GO:0034742 from "Related" to "Narrow"
  * Copied GO:0034742 to GO:0044444 with type OBO_REL:is_a
  * Copied GO:0034742 to GO:0043234 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034742
* Populated new object GO:0034743 (macro)
  * Changed name of GO:0034743 from "<new term>" to "APC-IQGAP complex"
  * Added comment "Note that the gene/protein name 'APC' should not be confused with the abbreviation for 'anaphase promoting complex'."
  * Set definition of GO:0034743 to "A protein complex that contains the tumor suppressor protein adenomatous polyposis coli (APC) and the Rac1 and Cdc42 effector IQGAP1; may play a role in cytoskeleton organization and cell migration."
  * Added definition dbxref PMID:15572129 to GO:0034743
  * Copied GO:0034743 to GO:0044444 with type OBO_REL:is_a
  * Copied GO:0034743 to GO:0043234 with type OBO_REL:is_a
  * Copied GO:0034743 to GO:0031252 with type part_of
  * Assigned namespace "cellular_component" to GO:0034743
* Populated new object GO:0034744 (macro)
  * Changed name of GO:0034744 from "<new term>" to "APC-IQGAP1-Cdc42 complex"
  * Added comment "Note that the gene/protein name 'APC' should not be confused with the abbreviation for 'anaphase promoting complex'."
  * Set definition of GO:0034744 to "A protein complex that contains the tumor suppressor protein adenomatous polyposis coli (APC), the small GTPase Cdc42, and the Rac1 and Cdc42 effector IQGAP1; may play a role in cytoskeleton organization and cell migration."
  * Added definition dbxref PMID:15572129 to GO:0034744
  * Copied GO:0034744 to GO:0044444 with type OBO_REL:is_a
  * Copied GO:0034744 to GO:0031252 with type part_of
  * Copied GO:0034744 to GO:0043234 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034744
* Populated new object GO:0034745 (macro)
  * Changed name of GO:0034745 from "<new term>" to "APC-IQGAP1-Rac1 complex"
  * Added comment "Note that the gene/protein name 'APC' should not be confused with the abbreviation for 'anaphase promoting complex'."
  * Set definition of GO:0034745 to "A protein complex that contains the tumor suppressor protein adenomatous polyposis coli (APC), the small GTPase Rac1, and the Rac1 and Cdc42 effector IQGAP1; may play a role in cytoskeleton organization and cell migration."
  * Added definition dbxref PMID:15572129 to GO:0034745
  * Copied GO:0034745 to GO:0031252 with type part_of
  * Copied GO:0034745 to GO:0044444 with type OBO_REL:is_a
  * Copied GO:0034745 to GO:0043234 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034745
* Changed definition of GO:0000126 from "A transcription factor for eukaryotic RNA polymerase III promoters that is an RNA polymerase binding protein." to "A transcription factor complex that is involved in regulating transcription from RNA polymerase III (Pol III) promoters. TFIIIB contains the TATA-binding protein (TBP) and two Pol III-specific proteins, B'' and BRF."
* Deleted definition dbxref ISBN:0198547684 from GO:0000126
* Added definition dbxref PMID:11433012 to GO:0000126
* Changed definition of GO:0000127 from "A heterotrimeric transcription factor for eukaryotic RNA polymerase III promoters." to "A transcription factor complex that is involved in regulating transcription from RNA polymerase III (Pol III) promoters. TFIIIC contains three conserved subunits that associate with the proximal Pol III promoter element, and additional subunits that associate with sequence elements downstream of the promoter and are more diverged among species."
* Deleted definition dbxref ISBN:0198547684 from GO:0000127
* Added definition dbxref PMID:11433012 to GO:0000127
* Changed synonym scope of GO:0004313 from "Exact" to "Broad"
* Changed definition of GO:0004772 from "Catalysis of the reaction: acyl-CoA + cholesterol = CoA + cholesterol ester." to "Catalysis of the reaction: acyl-CoA + a sterol = CoA + a sterol ester."
* Added definition dbxref GOC:mah to GO:0004772
* Deleted general dbxref EC:2.3.1.26 from GO:0004772
* Deleted general dbxref MetaCyc:STEROL-O-ACYLTRANSFERASE-RXN from GO:0004772
* Deleted synonym "ACAT" from GO:0004772
* Deleted synonym "acyl coenzyme A-cholesterol-O-acyltransferase activity" from GO:0004772
* Deleted synonym "acyl-CoA:cholesterol acyltransferase activity" from GO:0004772
* Deleted synonym "acyl-CoA:cholesterol O-acyltransferase activity" from GO:0004772
* Deleted synonym "acylcoenzyme A:cholesterol O-acyltransferase activity" from GO:0004772
* Deleted synonym "cholesterol acyltransferase activity" from GO:0004772
* Deleted synonym "cholesterol ester synthetase activity" from GO:0004772
* Deleted synonym "cholesterol O-acyltransferase activity" from GO:0004772
* Deleted synonym "cholesteryl ester synthetase activity" from GO:0004772
* Added comment "Note that the synonym 'APC' should not be confused with the abbreviation for the adenomatous polyposis coli gene and protein."
* Changed synonym scope of GO:0005680 from "Exact" to "Broad"
* Changed definition of GO:0016513 from "A heterodimer with alpha- and beta-subunits that binds the core site 5'-PYGPYGGT-3' of several enhancers and promoters; the beta-subunit enhances the DNA binding of the alpha-subunit." to "A heterodimeric transcription factor complex that contains an alpha subunit (Runx1, Runx2 or Runx3 in human) that binds DNA and a non-DNA-binding beta subunit (CBFbeta), and binds to a consensus sequence  5'-YGYGGTY-3' found in several enhancers and promoters; the beta subunit enhances the DNA binding of the alpha subunit."
* Deleted definition dbxref UniProtKB:Q08024 from GO:0016513
* Added definition dbxref PMID:15156179 to GO:0016513
* Added definition dbxref PMID:8497254 to GO:0016513
* Added synonym "AML1 complex" to GO:0016513
* Changed synonym scope of GO:0016513 from "Related" to "Narrow"
* Added synonym "CBF complex" to GO:0016513
* Changed synonym scope of GO:0016513 from "Related" to "Exact"
* Added synonym "PEPB2 complex" to GO:0016513
* Changed synonym scope of GO:0016513 from "Related" to "Narrow"
* Deleted GO:0033276 --OBO_REL:is_a--> GO:0043234
* Copied GO:0033276 to GO:0005667 with type OBO_REL:is_a
* Deleted synonym "macromolecular complex subunit organisation" from GO:0043933

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